Merge pull request #15 from O-Labz/memory-management-bug-fixes

fixed bugs

Author: HopsonO

src/core/indexer.ts

@@ -242,37 +242,36 @@ export class Indexer extends EventEmitter {
         parsed = await parseFile(relativePath, repositoryId, this.workspaceRoot);
       }
 
-      // Batch all graph writes in a single transaction for atomicity + performance
+      // Remove existing nodes from file before adding new ones
       await this.graph.removeNodesInFile(relativePath);
 
-      await this.storage.transaction(async () => {
-        // Bulk persist nodes (so resolveEdges' findByName lookups see them)
-        await this.graph.bulkLoad(parsed.nodes, []);
-        
-        // Resolve edges now that nodes are persisted
-        const edges = this.resolveEdges(parsed, repositoryId);
-        
-        // Bulk persist edges (single cache invalidation)
-        await this.graph.bulkLoad([], edges);
-
-        // Track pending forward references
-        this.pendingReferences.push({
-          calls: parsed.calls,
-          imports: parsed.imports,
-          inheritance: parsed.inheritance,
-          repositoryId,
-          filePath: parsed.filePath,
-        });
+      // Bulk persist nodes (so resolveEdges' findByName lookups see them)
+      await this.graph.bulkLoad(parsed.nodes, []);
+      
+      // Resolve edges now that nodes are persisted
+      const edges = this.resolveEdges(parsed, repositoryId);
+      
+      // Bulk persist edges (single cache invalidation)
+      await this.graph.bulkLoad([], edges);
+
+      // Track pending forward references
+      this.pendingReferences.push({
+        calls: parsed.calls,
+        imports: parsed.imports,
+        inheritance: parsed.inheritance,
+        repositoryId,
+        filePath: parsed.filePath,
+      });
 
-        // Update file metadata
+      // Update file metadata in a transaction
+      this.storage.transaction(() => {
         fileMetadata.hash = parsed.hash;
         fileMetadata.language = parsed.language;
         fileMetadata.nodeCount = parsed.nodes.length;
         fileMetadata.status = 'indexed';
         fileMetadata.lastError = undefined;
         fileMetadata.indexedAt = new Date();
         fileMetadata.updatedAt = new Date();
-
         fileMetadata.embeddingStatus = 'pending';
         this.storage.upsertFile(fileMetadata);
       });